QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-bwaters2' [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [I] RUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue May 30 18:07:40 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1433900296688 [I] ASSIGN makecnspec = -3 [I] ASSIGN makecnspec(1) = -3 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 3 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 15 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 3 [I] ASSIGN makecnspec(11) = 1 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -3 -1 1 -3 1 1 2 0 3]; basis=[ 0.909091 0 0.227273 0 0 0.681818 0.5 0.0454545 0 1 0.863636 0.5 0.0909091 0 2 0.772727 0.5 0.318182 0 3 0.954545 0.5 0.363636 0 4 0.863636 0.5 0.590909 0 5 0.954545 0.5 0.863636 0 6 0.545455 0 0.136364 0 7 0.727273 0 0.181818 0 8 0.636364 0 0.409091 0 9 0.818182 0 0.454545 0 10 0.727273 0 0.681818 0 11 0.909091 0 0.727273 0 12 0.818182 0 0.954545 0 13 0.5 0.5 0 0 14 0.409091 0.5 0.227273 0 15 0.590909 0.5 0.272727 0 16 0.5 0.5 0.5 0 17 0.681818 0.5 0.545455 0 18 0.590909 0.5 0.772727 0 19 0.772727 0.5 0.818182 0 20 0.181818 0 0.0454545 0 21 0.363636 0 0.0909091 0 22 0.272727 0 0.318182 0 23 0.454545 0 0.363636 0 24 0.363636 0 0.590909 0 25 0.545455 0 0.636364 0 26 0.454545 0 0.863636 0 27 0.636364 0 0.909091 0 28 0.0454545 0.5 0.136364 0 29 0.227273 0.5 0.181818 0 30 0.136364 0.5 0.409091 0 31 0.318182 0.5 0.454545 0 32 0.227273 0.5 0.681818 0 33 0.409091 0.5 0.727273 0 34 0.318182 0.5 0.954545 0 35 0 0 0 0 36 0.0909091 0 0.272727 0 37 0 0 0.5 0 38 0.181818 0 0.545455 0 39 0.0909091 0 0.772727 0 40 0.272727 0 0.818182 0 41 0.0454545 0.5 0.636364 0 42 0.136364 0.5 0.909091 0 43 ]; [I] makecn: _NP=1980 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.03030303030303 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.22727272727273 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27878513552049 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 3.0303030303e-02 -0.0000000000e+00 -2.2727272727e-01 b= 1.3403460122e+00 0.0000000000e+00 -2.3694193859e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.3403460122209 by=0 pxpa=4.423142e+01 pxpb=0.000000e+00 pypb=6.668137e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 850 need remove atom 853 need remove atom 860 need remove atom 863 need remove atom 894 need remove atom 897 need remove atom 904 need remove atom 907 need remove atom 938 need remove atom 941 need remove atom 948 need remove atom 951 need remove atom 982 need remove atom 985 need remove atom 992 need remove atom 995 need remove atom 1026 need remove atom 1029 need remove atom 1036 need remove atom 1039 need remove atom 1070 need remove atom 1073 need remove atom 1080 need remove atom 1083 need remove atom 1114 need remove atom 1117 need remove atom 1124 need remove atom 1127 need remove atom 1168 need remove atom 1171 [I] need removenum=30 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 2.7200239548e-01 8.5293435575e-02 -3.6854575150e-01 dub= -2.8527311756e-01 8.5295345813e-02 3.7535937294e-01 duc= 2.7200316756e-01 -8.6393793339e-02 -3.6854693353e-01 [I] overall tilt ux= -5.5727551304e-01 1.9102376690e-06 7.4390512444e-01 uy= 7.7207491295e-07 -1.7168722891e-01 -1.1820266749e-06 [I] storedr[0]= -3.0813725876e-02 -4.7052412576e-04 -5.9718131902e-02 [I] originally 1980 atoms [I] insert 0 atoms [I] now 1980 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 1980 atoms [I] remove 30 atoms [I] now 1950 atoms [I] NP=1950 n=1950 [I] ASSIGN finalcnfile = dipole_1.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 18:07:41 2023 CPU time spent: 0.166687 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue May 30 18:08:33 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1433900296688 [I] ASSIGN makecnspec = -3 [I] ASSIGN makecnspec(1) = -3 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 3 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 15 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 3 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -3 -1 1 -3 1 1 2 0 3]; basis=[ 0.909091 0 0.227273 0 0 0.681818 0.5 0.0454545 0 1 0.863636 0.5 0.0909091 0 2 0.772727 0.5 0.318182 0 3 0.954545 0.5 0.363636 0 4 0.863636 0.5 0.590909 0 5 0.954545 0.5 0.863636 0 6 0.545455 0 0.136364 0 7 0.727273 0 0.181818 0 8 0.636364 0 0.409091 0 9 0.818182 0 0.454545 0 10 0.727273 0 0.681818 0 11 0.909091 0 0.727273 0 12 0.818182 0 0.954545 0 13 0.5 0.5 0 0 14 0.409091 0.5 0.227273 0 15 0.590909 0.5 0.272727 0 16 0.5 0.5 0.5 0 17 0.681818 0.5 0.545455 0 18 0.590909 0.5 0.772727 0 19 0.772727 0.5 0.818182 0 20 0.181818 0 0.0454545 0 21 0.363636 0 0.0909091 0 22 0.272727 0 0.318182 0 23 0.454545 0 0.363636 0 24 0.363636 0 0.590909 0 25 0.545455 0 0.636364 0 26 0.454545 0 0.863636 0 27 0.636364 0 0.909091 0 28 0.0454545 0.5 0.136364 0 29 0.227273 0.5 0.181818 0 30 0.136364 0.5 0.409091 0 31 0.318182 0.5 0.454545 0 32 0.227273 0.5 0.681818 0 33 0.409091 0.5 0.727273 0 34 0.318182 0.5 0.954545 0 35 0 0 0 0 36 0.0909091 0 0.272727 0 37 0 0 0.5 0 38 0.181818 0 0.545455 0 39 0.0909091 0 0.772727 0 40 0.272727 0 0.818182 0 41 0.0454545 0.5 0.636364 0 42 0.136364 0.5 0.909091 0 43 ]; [I] makecn: _NP=3960 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.03030303030303 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.11363636363636 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27878513552049 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 3.0303030303e-02 -0.0000000000e+00 -1.1363636364e-01 b= 1.3403460122e+00 0.0000000000e+00 -2.3694193859e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.3403460122209 by=0 pxpa=4.423142e+01 pxpb=0.000000e+00 pypb=6.668137e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1686 need remove atom 1689 need remove atom 1696 need remove atom 1699 need remove atom 1730 need remove atom 1733 need remove atom 1740 need remove atom 1743 need remove atom 1774 need remove atom 1777 need remove atom 1784 need remove atom 1787 need remove atom 1818 need remove atom 1821 need remove atom 1828 need remove atom 1831 need remove atom 1862 need remove atom 1865 need remove atom 1872 need remove atom 1875 need remove atom 1906 need remove atom 1909 need remove atom 1916 need remove atom 1919 need remove atom 1950 need remove atom 1953 need remove atom 1960 need remove atom 1963 need remove atom 1994 need remove atom 1997 need remove atom 2004 need remove atom 2007 need remove atom 2038 need remove atom 2041 need remove atom 2048 need remove atom 2051 need remove atom 2082 need remove atom 2085 need remove atom 2092 need remove atom 2095 need remove atom 2126 need remove atom 2129 need remove atom 2136 need remove atom 2139 need remove atom 2170 need remove atom 2173 need remove atom 2180 need remove atom 2183 need remove atom 2214 need remove atom 2217 need remove atom 2224 need remove atom 2227 need remove atom 2258 need remove atom 2261 need remove atom 2268 need remove atom 2271 need remove atom 2312 need remove atom 2315 need remove atom 2356 need remove atom 2359 [I] need removenum=60 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 2.7200239548e-01 8.5293435575e-02 -3.6854575150e-01 dub= -2.8527311756e-01 8.5295345813e-02 3.7535937294e-01 duc= 2.7200316756e-01 -8.6393793339e-02 -3.6854693353e-01 [I] overall tilt ux= -5.5727551304e-01 1.9102376690e-06 7.4390512444e-01 uy= 7.7207491295e-07 -1.7168722891e-01 -1.1820266749e-06 [I] storedr[0]= -3.0813725876e-02 -4.7052412576e-04 -5.9718131902e-02 [I] originally 3960 atoms [I] insert 0 atoms [I] now 3960 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 3960 atoms [I] remove 60 atoms [I] now 3900 atoms [I] NP=3900 n=3900 [I] ASSIGN finalcnfile = dipole_1.2.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.2.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.2.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 18:08:33 2023 CPU time spent: 0.336186 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue May 30 18:09:42 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1433900296688 [I] ASSIGN makecnspec = -3 [I] ASSIGN makecnspec(1) = -3 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 4 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 20 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 3 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -3 -1 1 -3 1 1 2 0 3]; basis=[ 0.909091 0 0.227273 0 0 0.681818 0.5 0.0454545 0 1 0.863636 0.5 0.0909091 0 2 0.772727 0.5 0.318182 0 3 0.954545 0.5 0.363636 0 4 0.863636 0.5 0.590909 0 5 0.954545 0.5 0.863636 0 6 0.545455 0 0.136364 0 7 0.727273 0 0.181818 0 8 0.636364 0 0.409091 0 9 0.818182 0 0.454545 0 10 0.727273 0 0.681818 0 11 0.909091 0 0.727273 0 12 0.818182 0 0.954545 0 13 0.5 0.5 0 0 14 0.409091 0.5 0.227273 0 15 0.590909 0.5 0.272727 0 16 0.5 0.5 0.5 0 17 0.681818 0.5 0.545455 0 18 0.590909 0.5 0.772727 0 19 0.772727 0.5 0.818182 0 20 0.181818 0 0.0454545 0 21 0.363636 0 0.0909091 0 22 0.272727 0 0.318182 0 23 0.454545 0 0.363636 0 24 0.363636 0 0.590909 0 25 0.545455 0 0.636364 0 26 0.454545 0 0.863636 0 27 0.636364 0 0.909091 0 28 0.0454545 0.5 0.136364 0 29 0.227273 0.5 0.181818 0 30 0.136364 0.5 0.409091 0 31 0.318182 0.5 0.454545 0 32 0.227273 0.5 0.681818 0 33 0.409091 0.5 0.727273 0 34 0.318182 0.5 0.954545 0 35 0 0 0 0 36 0.0909091 0 0.272727 0 37 0 0 0.5 0 38 0.181818 0 0.545455 0 39 0.0909091 0 0.772727 0 40 0.272727 0 0.818182 0 41 0.0454545 0.5 0.636364 0 42 0.136364 0.5 0.909091 0 43 ]; [I] makecn: _NP=7040 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.022727272727273 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.11363636363636 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27878513552049 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 2.2727272727e-02 -0.0000000000e+00 -1.1363636364e-01 b= 1.3403460122e+00 0.0000000000e+00 -2.3694193859e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.3403460122209 by=0 pxpa=5.897522e+01 pxpb=0.000000e+00 pypb=8.890850e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 2204 need remove atom 2206 need remove atom 2248 need remove atom 2250 need remove atom 2292 need remove atom 2294 need remove atom 2336 need remove atom 2338 need remove atom 2380 need remove atom 2382 need remove atom 2424 need remove atom 2426 need remove atom 2468 need remove atom 2470 need remove atom 2512 need remove atom 2514 need remove atom 2556 need remove atom 2558 need remove atom 2600 need remove atom 2602 need remove atom 2644 need remove atom 2646 need remove atom 2688 need remove atom 2690 need remove atom 2732 need remove atom 2734 need remove atom 2776 need remove atom 2778 need remove atom 2820 need remove atom 2822 need remove atom 2864 need remove atom 2866 need remove atom 2908 need remove atom 2910 need remove atom 2952 need remove atom 2954 need remove atom 2996 need remove atom 2998 need remove atom 3040 need remove atom 3042 need remove atom 4084 need remove atom 4086 need remove atom 4128 need remove atom 4130 need remove atom 4172 need remove atom 4174 need remove atom 4216 need remove atom 4218 need remove atom 4260 need remove atom 4262 need remove atom 4304 need remove atom 4306 need remove atom 4348 need remove atom 4350 need remove atom 4392 need remove atom 4394 need remove atom 4436 need remove atom 4438 need remove atom 4480 need remove atom 4482 need remove atom 4524 need remove atom 4526 need remove atom 4568 need remove atom 4570 need remove atom 4612 need remove atom 4614 need remove atom 4656 need remove atom 4658 need remove atom 4700 need remove atom 4702 need remove atom 4744 need remove atom 4746 need remove atom 4788 need remove atom 4790 need remove atom 4832 need remove atom 4834 need remove atom 4876 need remove atom 4878 need remove atom 4920 need remove atom 4922 [I] need removenum=80 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 2.7200239548e-01 8.5293435575e-02 -3.6854575150e-01 dub= -2.8527311756e-01 8.5295345813e-02 3.7535937294e-01 duc= 2.7200316756e-01 -8.6393793339e-02 -3.6854693353e-01 [I] overall tilt ux= -5.5727551304e-01 1.9102376684e-06 7.4390512444e-01 uy= 7.7207491306e-07 -1.7168722891e-01 -1.1820266759e-06 [I] storedr[0]= -2.8661338677e-02 -5.2959657350e-04 -6.1924146687e-02 [I] originally 7040 atoms [I] insert 0 atoms [I] now 7040 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 7040 atoms [I] remove 80 atoms [I] now 6960 atoms [I] NP=6960 n=6960 [I] ASSIGN finalcnfile = dipole_1.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 18:09:42 2023 CPU time spent: 0.604667 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue May 30 18:10:26 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1433900296688 [I] ASSIGN makecnspec = -3 [I] ASSIGN makecnspec(1) = -3 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 5 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 25 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 3 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -3 -1 1 -3 1 1 2 0 3]; basis=[ 0.909091 0 0.227273 0 0 0.681818 0.5 0.0454545 0 1 0.863636 0.5 0.0909091 0 2 0.772727 0.5 0.318182 0 3 0.954545 0.5 0.363636 0 4 0.863636 0.5 0.590909 0 5 0.954545 0.5 0.863636 0 6 0.545455 0 0.136364 0 7 0.727273 0 0.181818 0 8 0.636364 0 0.409091 0 9 0.818182 0 0.454545 0 10 0.727273 0 0.681818 0 11 0.909091 0 0.727273 0 12 0.818182 0 0.954545 0 13 0.5 0.5 0 0 14 0.409091 0.5 0.227273 0 15 0.590909 0.5 0.272727 0 16 0.5 0.5 0.5 0 17 0.681818 0.5 0.545455 0 18 0.590909 0.5 0.772727 0 19 0.772727 0.5 0.818182 0 20 0.181818 0 0.0454545 0 21 0.363636 0 0.0909091 0 22 0.272727 0 0.318182 0 23 0.454545 0 0.363636 0 24 0.363636 0 0.590909 0 25 0.545455 0 0.636364 0 26 0.454545 0 0.863636 0 27 0.636364 0 0.909091 0 28 0.0454545 0.5 0.136364 0 29 0.227273 0.5 0.181818 0 30 0.136364 0.5 0.409091 0 31 0.318182 0.5 0.454545 0 32 0.227273 0.5 0.681818 0 33 0.409091 0.5 0.727273 0 34 0.318182 0.5 0.954545 0 35 0 0 0 0 36 0.0909091 0 0.272727 0 37 0 0 0.5 0 38 0.181818 0 0.545455 0 39 0.0909091 0 0.772727 0 40 0.272727 0 0.818182 0 41 0.0454545 0.5 0.636364 0 42 0.136364 0.5 0.909091 0 43 ]; [I] makecn: _NP=11000 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.018181818181818 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.11363636363636 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27878513552049 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.8181818182e-02 -0.0000000000e+00 -1.1363636364e-01 b= 1.3403460122e+00 0.0000000000e+00 -2.3694193859e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.3403460122209 by=0 pxpa=7.371903e+01 pxpb=0.000000e+00 pypb=1.111356e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 4943 need remove atom 4962 need remove atom 4987 need remove atom 5006 need remove atom 5031 need remove atom 5040 need remove atom 5043 need remove atom 5050 need remove atom 5075 need remove atom 5084 need remove atom 5087 need remove atom 5094 need remove atom 5119 need remove atom 5128 need remove atom 5131 need remove atom 5138 need remove atom 5163 need remove atom 5172 need remove atom 5175 need remove atom 5182 need remove atom 5207 need remove atom 5216 need remove atom 5219 need remove atom 5226 need remove atom 5251 need remove atom 5260 need remove atom 5263 need remove atom 5270 need remove atom 5295 need remove atom 5304 need remove atom 5307 need remove atom 5314 need remove atom 5339 need remove atom 5348 need remove atom 5351 need remove atom 5358 need remove atom 5383 need remove atom 5392 need remove atom 5395 need remove atom 5402 need remove atom 5427 need remove atom 5436 need remove atom 5439 need remove atom 5446 need remove atom 5471 need remove atom 5480 need remove atom 5483 need remove atom 5490 need remove atom 5515 need remove atom 5524 need remove atom 5527 need remove atom 5534 need remove atom 5559 need remove atom 5568 need remove atom 5571 need remove atom 5578 need remove atom 5603 need remove atom 5612 need remove atom 5615 need remove atom 5622 need remove atom 5647 need remove atom 5656 need remove atom 5659 need remove atom 5666 need remove atom 5691 need remove atom 5700 need remove atom 5703 need remove atom 5710 need remove atom 5735 need remove atom 5744 need remove atom 5747 need remove atom 5754 need remove atom 5779 need remove atom 5788 need remove atom 5791 need remove atom 5798 need remove atom 5823 need remove atom 5832 need remove atom 5835 need remove atom 5842 need remove atom 5867 need remove atom 5876 need remove atom 5879 need remove atom 5886 need remove atom 5911 need remove atom 5920 need remove atom 5923 need remove atom 5930 need remove atom 5955 need remove atom 5964 need remove atom 5967 need remove atom 5974 need remove atom 5999 need remove atom 6008 need remove atom 6011 need remove atom 6018 need remove atom 6043 need remove atom 6052 need remove atom 6055 need remove atom 6062 [I] need removenum=100 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 2.7200239548e-01 8.5293435575e-02 -3.6854575150e-01 dub= -2.8527311756e-01 8.5295345813e-02 3.7535937294e-01 duc= 2.7200316756e-01 -8.6393793339e-02 -3.6854693353e-01 [I] overall tilt ux= -5.5727551304e-01 1.9102376688e-06 7.4390512444e-01 uy= 7.7207491295e-07 -1.7168722891e-01 -1.1820266758e-06 [I] storedr[0]= -2.5213934776e-02 -5.4741790811e-04 -5.5921395031e-02 [I] originally 11000 atoms [I] insert 0 atoms [I] now 11000 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 11000 atoms [I] remove 100 atoms [I] now 10900 atoms [I] NP=10900 n=10900 [I] ASSIGN finalcnfile = dipole_1.9.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.9.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.9.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 18:10:27 2023 CPU time spent: 0.922307 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue May 30 18:11:21 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1433900296688 [I] ASSIGN makecnspec = -3 [I] ASSIGN makecnspec(1) = -3 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 6 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 30 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 3 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -3 -1 1 -3 1 1 2 0 3]; basis=[ 0.909091 0 0.227273 0 0 0.681818 0.5 0.0454545 0 1 0.863636 0.5 0.0909091 0 2 0.772727 0.5 0.318182 0 3 0.954545 0.5 0.363636 0 4 0.863636 0.5 0.590909 0 5 0.954545 0.5 0.863636 0 6 0.545455 0 0.136364 0 7 0.727273 0 0.181818 0 8 0.636364 0 0.409091 0 9 0.818182 0 0.454545 0 10 0.727273 0 0.681818 0 11 0.909091 0 0.727273 0 12 0.818182 0 0.954545 0 13 0.5 0.5 0 0 14 0.409091 0.5 0.227273 0 15 0.590909 0.5 0.272727 0 16 0.5 0.5 0.5 0 17 0.681818 0.5 0.545455 0 18 0.590909 0.5 0.772727 0 19 0.772727 0.5 0.818182 0 20 0.181818 0 0.0454545 0 21 0.363636 0 0.0909091 0 22 0.272727 0 0.318182 0 23 0.454545 0 0.363636 0 24 0.363636 0 0.590909 0 25 0.545455 0 0.636364 0 26 0.454545 0 0.863636 0 27 0.636364 0 0.909091 0 28 0.0454545 0.5 0.136364 0 29 0.227273 0.5 0.181818 0 30 0.136364 0.5 0.409091 0 31 0.318182 0.5 0.454545 0 32 0.227273 0.5 0.681818 0 33 0.409091 0.5 0.727273 0 34 0.318182 0.5 0.954545 0 35 0 0 0 0 36 0.0909091 0 0.272727 0 37 0 0 0.5 0 38 0.181818 0 0.545455 0 39 0.0909091 0 0.772727 0 40 0.272727 0 0.818182 0 41 0.0454545 0.5 0.636364 0 42 0.136364 0.5 0.909091 0 43 ]; [I] makecn: _NP=23760 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.015151515151515 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.075757575757576 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27878513552049 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.5151515152e-02 -0.0000000000e+00 -7.5757575758e-02 b= 1.3403460122e+00 0.0000000000e+00 -2.3694193859e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.3403460122209 by=0 pxpa=8.846284e+01 pxpb=0.000000e+00 pypb=1.333627e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 8976 need remove atom 8980 need remove atom 8982 need remove atom 8988 need remove atom 9020 need remove atom 9024 need remove atom 9026 need remove atom 9032 need remove atom 9064 need remove atom 9068 need remove atom 9070 need remove atom 9076 need remove atom 9108 need remove atom 9112 need remove atom 9114 need remove atom 9120 need remove atom 9152 need remove atom 9156 need remove atom 9158 need remove atom 9164 need remove atom 9196 need remove atom 9200 need remove atom 9202 need remove atom 9208 need remove atom 9240 need remove atom 9244 need remove atom 9246 need remove atom 9252 need remove atom 9284 need remove atom 9288 need remove atom 9290 need remove atom 9296 need remove atom 9328 need remove atom 9332 need remove atom 9334 need remove atom 9340 need remove atom 9372 need remove atom 9376 need remove atom 9378 need remove atom 9384 need remove atom 9416 need remove atom 9420 need remove atom 9422 need remove atom 9428 need remove atom 9460 need remove atom 9464 need remove atom 9466 need remove atom 9472 need remove atom 9504 need remove atom 9508 need remove atom 9510 need remove atom 9516 need remove atom 9548 need remove atom 9552 need remove atom 9554 need remove atom 9560 need remove atom 9592 need remove atom 9596 need remove atom 9598 need remove atom 9604 need remove atom 9636 need remove atom 9640 need remove atom 9642 need remove atom 9648 need remove atom 9680 need remove atom 9684 need remove atom 9686 need remove atom 9692 need remove atom 9724 need remove atom 9728 need remove atom 9730 need remove atom 9736 need remove atom 9768 need remove atom 9772 need remove atom 9774 need remove atom 9780 need remove atom 9812 need remove atom 9816 need remove atom 9818 need remove atom 9824 need remove atom 9856 need remove atom 9860 need remove atom 9862 need remove atom 9868 need remove atom 9900 need remove atom 9904 need remove atom 9906 need remove atom 9912 need remove atom 9944 need remove atom 9948 need remove atom 9950 need remove atom 9956 need remove atom 9988 need remove atom 9992 need remove atom 9994 need remove atom 10000 need remove atom 10032 need remove atom 10036 need remove atom 10038 need remove atom 10044 need remove atom 10076 need remove atom 10080 need remove atom 10082 need remove atom 10088 need remove atom 10120 need remove atom 10124 need remove atom 10126 need remove atom 10132 need remove atom 10164 need remove atom 10168 need remove atom 10170 need remove atom 10176 need remove atom 10208 need remove atom 10212 need remove atom 10214 need remove atom 10220 need remove atom 10252 need remove atom 10256 need remove atom 10258 need remove atom 10264 need remove atom 10296 need remove atom 10300 need remove atom 10302 need remove atom 10308 need remove atom 10340 need remove atom 10344 need remove atom 10346 need remove atom 10352 need remove atom 10384 need remove atom 10388 need remove atom 10390 need remove atom 10396 need remove atom 10428 need remove atom 10432 need remove atom 10434 need remove atom 10440 need remove atom 10472 need remove atom 10476 need remove atom 10478 need remove atom 10484 need remove atom 10516 need remove atom 10520 need remove atom 10522 need remove atom 10528 need remove atom 10560 need remove atom 10564 need remove atom 10566 need remove atom 10572 need remove atom 10604 need remove atom 10608 need remove atom 10610 need remove atom 10616 need remove atom 10648 need remove atom 10652 need remove atom 10654 need remove atom 10660 need remove atom 10692 need remove atom 10696 need remove atom 10698 need remove atom 10704 need remove atom 10736 need remove atom 10740 need remove atom 10742 need remove atom 10748 need remove atom 10780 need remove atom 10784 need remove atom 10786 need remove atom 10792 need remove atom 10824 need remove atom 10828 need remove atom 10830 need remove atom 10836 need remove atom 10868 need remove atom 10872 need remove atom 10874 need remove atom 10880 need remove atom 10912 need remove atom 10916 need remove atom 10918 need remove atom 10924 [I] need removenum=180 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 2.7200239548e-01 8.5293435575e-02 -3.6854575150e-01 dub= -2.8527311756e-01 8.5295345813e-02 3.7535937294e-01 duc= 2.7200316756e-01 -8.6393793339e-02 -3.6854693353e-01 [I] overall tilt ux= -5.5727551304e-01 1.9102376690e-06 7.4390512444e-01 uy= 7.7207491395e-07 -1.7168722891e-01 -1.1820266747e-06 [I] storedr[0]= -2.2422424760e-02 -5.5338513195e-04 -4.9325522254e-02 [I] originally 23760 atoms [I] insert 0 atoms [I] now 23760 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 23760 atoms [I] remove 180 atoms [I] now 23580 atoms [I] NP=23580 n=23580 [I] ASSIGN finalcnfile = dipole_2.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_2.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_2.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 18:11:23 2023 CPU time spent: 2.019890 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue May 30 18:12:50 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1433900296688 [I] ASSIGN makecnspec = -3 [I] ASSIGN makecnspec(1) = -3 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 7 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 35 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 3 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -3 -1 1 -3 1 1 2 0 3]; basis=[ 0.909091 0 0.227273 0 0 0.681818 0.5 0.0454545 0 1 0.863636 0.5 0.0909091 0 2 0.772727 0.5 0.318182 0 3 0.954545 0.5 0.363636 0 4 0.863636 0.5 0.590909 0 5 0.954545 0.5 0.863636 0 6 0.545455 0 0.136364 0 7 0.727273 0 0.181818 0 8 0.636364 0 0.409091 0 9 0.818182 0 0.454545 0 10 0.727273 0 0.681818 0 11 0.909091 0 0.727273 0 12 0.818182 0 0.954545 0 13 0.5 0.5 0 0 14 0.409091 0.5 0.227273 0 15 0.590909 0.5 0.272727 0 16 0.5 0.5 0.5 0 17 0.681818 0.5 0.545455 0 18 0.590909 0.5 0.772727 0 19 0.772727 0.5 0.818182 0 20 0.181818 0 0.0454545 0 21 0.363636 0 0.0909091 0 22 0.272727 0 0.318182 0 23 0.454545 0 0.363636 0 24 0.363636 0 0.590909 0 25 0.545455 0 0.636364 0 26 0.454545 0 0.863636 0 27 0.636364 0 0.909091 0 28 0.0454545 0.5 0.136364 0 29 0.227273 0.5 0.181818 0 30 0.136364 0.5 0.409091 0 31 0.318182 0.5 0.454545 0 32 0.227273 0.5 0.681818 0 33 0.409091 0.5 0.727273 0 34 0.318182 0.5 0.954545 0 35 0 0 0 0 36 0.0909091 0 0.272727 0 37 0 0 0.5 0 38 0.181818 0 0.545455 0 39 0.0909091 0 0.772727 0 40 0.272727 0 0.818182 0 41 0.0454545 0.5 0.636364 0 42 0.136364 0.5 0.909091 0 43 ]; [I] makecn: _NP=32340 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.012987012987013 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.075757575757576 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27878513552049 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.2987012987e-02 -0.0000000000e+00 -7.5757575758e-02 b= 1.3403460122e+00 0.0000000000e+00 -2.3694193859e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.3403460122209 by=0 pxpa=1.032066e+02 pxpb=0.000000e+00 pypb=1.555899e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 15063 need remove atom 15072 need remove atom 15075 need remove atom 15082 need remove atom 15107 need remove atom 15116 need remove atom 15119 need remove atom 15126 need remove atom 15151 need remove atom 15160 need remove atom 15163 need remove atom 15170 need remove atom 15195 need remove atom 15204 need remove atom 15207 need remove atom 15214 need remove atom 15239 need remove atom 15248 need remove atom 15251 need remove atom 15258 need remove atom 15283 need remove atom 15292 need remove atom 15295 need remove atom 15302 need remove atom 15327 need remove atom 15336 need remove atom 15339 need remove atom 15346 need remove atom 15371 need remove atom 15380 need remove atom 15383 need remove atom 15390 need remove atom 15415 need remove atom 15424 need remove atom 15427 need remove atom 15434 need remove atom 15459 need remove atom 15468 need remove atom 15471 need remove atom 15478 need remove atom 15503 need remove atom 15512 need remove atom 15515 need remove atom 15522 need remove atom 15547 need remove atom 15556 need remove atom 15559 need remove atom 15566 need remove atom 15591 need remove atom 15600 need remove atom 15603 need remove atom 15610 need remove atom 15635 need remove atom 15644 need remove atom 15647 need remove atom 15654 need remove atom 15679 need remove atom 15688 need remove atom 15691 need remove atom 15698 need remove atom 15723 need remove atom 15732 need remove atom 15735 need remove atom 15742 need remove atom 15767 need remove atom 15776 need remove atom 15779 need remove atom 15786 need remove atom 15811 need remove atom 15820 need remove atom 15823 need remove atom 15830 need remove atom 15855 need remove atom 15864 need remove atom 15867 need remove atom 15874 need remove atom 15899 need remove atom 15908 need remove atom 15911 need remove atom 15918 need remove atom 15943 need remove atom 15952 need remove atom 15955 need remove atom 15962 need remove atom 15987 need remove atom 15996 need remove atom 15999 need remove atom 16006 need remove atom 16031 need remove atom 16040 need remove atom 16043 need remove atom 16050 need remove atom 16075 need remove atom 16084 need remove atom 16087 need remove atom 16094 need remove atom 16119 need remove atom 16128 need remove atom 16131 need remove atom 16138 need remove atom 16163 need remove atom 16172 need remove atom 16175 need remove atom 16182 need remove atom 16207 need remove atom 16216 need remove atom 16219 need remove atom 16226 need remove atom 16251 need remove atom 16260 need remove atom 16263 need remove atom 16270 need remove atom 16295 need remove atom 16304 need remove atom 16307 need remove atom 16314 need remove atom 16339 need remove atom 16348 need remove atom 16351 need remove atom 16358 need remove atom 16383 need remove atom 16392 need remove atom 16395 need remove atom 16402 need remove atom 16427 need remove atom 16436 need remove atom 16439 need remove atom 16446 need remove atom 16471 need remove atom 16480 need remove atom 16483 need remove atom 16490 need remove atom 16515 need remove atom 16524 need remove atom 16527 need remove atom 16534 need remove atom 16559 need remove atom 16568 need remove atom 16571 need remove atom 16578 need remove atom 16603 need remove atom 16612 need remove atom 16615 need remove atom 16622 need remove atom 16647 need remove atom 16656 need remove atom 16659 need remove atom 16666 need remove atom 16691 need remove atom 16700 need remove atom 16703 need remove atom 16710 need remove atom 16735 need remove atom 16744 need remove atom 16747 need remove atom 16754 need remove atom 16779 need remove atom 16788 need remove atom 16791 need remove atom 16798 need remove atom 16823 need remove atom 16832 need remove atom 16835 need remove atom 16842 need remove atom 16867 need remove atom 16876 need remove atom 16879 need remove atom 16886 need remove atom 16911 need remove atom 16920 need remove atom 16923 need remove atom 16930 need remove atom 16955 need remove atom 16964 need remove atom 16967 need remove atom 16974 need remove atom 16999 need remove atom 17008 need remove atom 17011 need remove atom 17018 need remove atom 17043 need remove atom 17052 need remove atom 17055 need remove atom 17062 need remove atom 17087 need remove atom 17096 need remove atom 17099 need remove atom 17106 need remove atom 17131 need remove atom 17140 need remove atom 17143 need remove atom 17150 need remove atom 17175 need remove atom 17184 need remove atom 17187 need remove atom 17194 need remove atom 17219 need remove atom 17228 need remove atom 17231 need remove atom 17238 need remove atom 17263 need remove atom 17272 need remove atom 17275 need remove atom 17282 need remove atom 17316 need remove atom 17319 need remove atom 17360 need remove atom 17363 need remove atom 17404 need remove atom 17407 [I] need removenum=210 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 2.7200239548e-01 8.5293435575e-02 -3.6854575150e-01 dub= -2.8527311756e-01 8.5295345813e-02 3.7535937294e-01 duc= 2.7200316756e-01 -8.6393793339e-02 -3.6854693353e-01 [I] overall tilt ux= -5.5727551304e-01 1.9102376683e-06 7.4390512444e-01 uy= 7.7207491295e-07 -1.7168722891e-01 -1.1820266748e-06 [I] storedr[0]= -2.0284292652e-02 -5.5545019190e-04 -4.3529767891e-02 [I] originally 32340 atoms [I] insert 0 atoms [I] now 32340 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 32340 atoms [I] remove 210 atoms [I] now 32130 atoms [I] NP=32130 n=32130 [I] ASSIGN finalcnfile = dipole_3.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_3.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_3.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 18:12:53 2023 CPU time spent: 2.755479 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue May 30 18:14:38 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1433900296688 [I] ASSIGN makecnspec = -3 [I] ASSIGN makecnspec(1) = -3 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 8 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 40 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 3 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -3 -1 1 -3 1 1 2 0 3]; basis=[ 0.909091 0 0.227273 0 0 0.681818 0.5 0.0454545 0 1 0.863636 0.5 0.0909091 0 2 0.772727 0.5 0.318182 0 3 0.954545 0.5 0.363636 0 4 0.863636 0.5 0.590909 0 5 0.954545 0.5 0.863636 0 6 0.545455 0 0.136364 0 7 0.727273 0 0.181818 0 8 0.636364 0 0.409091 0 9 0.818182 0 0.454545 0 10 0.727273 0 0.681818 0 11 0.909091 0 0.727273 0 12 0.818182 0 0.954545 0 13 0.5 0.5 0 0 14 0.409091 0.5 0.227273 0 15 0.590909 0.5 0.272727 0 16 0.5 0.5 0.5 0 17 0.681818 0.5 0.545455 0 18 0.590909 0.5 0.772727 0 19 0.772727 0.5 0.818182 0 20 0.181818 0 0.0454545 0 21 0.363636 0 0.0909091 0 22 0.272727 0 0.318182 0 23 0.454545 0 0.363636 0 24 0.363636 0 0.590909 0 25 0.545455 0 0.636364 0 26 0.454545 0 0.863636 0 27 0.636364 0 0.909091 0 28 0.0454545 0.5 0.136364 0 29 0.227273 0.5 0.181818 0 30 0.136364 0.5 0.409091 0 31 0.318182 0.5 0.454545 0 32 0.227273 0.5 0.681818 0 33 0.409091 0.5 0.727273 0 34 0.318182 0.5 0.954545 0 35 0 0 0 0 36 0.0909091 0 0.272727 0 37 0 0 0.5 0 38 0.181818 0 0.545455 0 39 0.0909091 0 0.772727 0 40 0.272727 0 0.818182 0 41 0.0454545 0.5 0.636364 0 42 0.136364 0.5 0.909091 0 43 ]; [I] makecn: _NP=56320 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.011363636363636 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.056818181818182 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27878513552049 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.1363636364e-02 -0.0000000000e+00 -5.6818181818e-02 b= 1.3403460122e+00 0.0000000000e+00 -2.3694193859e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.3403460122209 by=0 pxpa=1.179504e+02 pxpb=0.000000e+00 pypb=1.778170e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 22884 need remove atom 22886 need remove atom 22928 need remove atom 22930 need remove atom 22972 need remove atom 22974 need remove atom 23016 need remove atom 23018 need remove atom 23056 need remove atom 23060 need remove atom 23062 need remove atom 23068 need remove atom 23100 need remove atom 23104 need remove atom 23106 need remove atom 23112 need remove atom 23144 need remove atom 23148 need remove atom 23150 need remove atom 23156 need remove atom 23188 need remove atom 23192 need remove atom 23194 need remove atom 23200 need remove atom 23232 need remove atom 23236 need remove atom 23238 need remove atom 23244 need remove atom 23276 need remove atom 23280 need remove atom 23282 need remove atom 23288 need remove atom 23320 need remove atom 23324 need remove atom 23326 need remove atom 23332 need remove atom 23364 need remove atom 23368 need remove atom 23370 need remove atom 23376 need remove atom 23408 need remove atom 23412 need remove atom 23414 need remove atom 23420 need remove atom 23452 need remove atom 23456 need remove atom 23458 need remove atom 23464 need remove atom 23496 need remove atom 23500 need remove atom 23502 need remove atom 23508 need remove atom 23540 need remove atom 23544 need remove atom 23546 need remove atom 23552 need remove atom 23584 need remove atom 23588 need remove atom 23590 need remove atom 23596 need remove atom 23628 need remove atom 23632 need remove atom 23634 need remove atom 23640 need remove atom 23672 need remove atom 23676 need remove atom 23678 need remove atom 23684 need remove atom 23716 need remove atom 23720 need remove atom 23722 need remove atom 23728 need remove atom 23760 need remove atom 23764 need remove atom 23766 need remove atom 23772 need remove atom 23804 need remove atom 23808 need remove atom 23810 need remove atom 23816 need remove atom 23848 need remove atom 23852 need remove atom 23854 need remove atom 23860 need remove atom 23892 need remove atom 23896 need remove atom 23898 need remove atom 23904 need remove atom 23936 need remove atom 23940 need remove atom 23942 need remove atom 23948 need remove atom 23980 need remove atom 23984 need remove atom 23986 need remove atom 23992 need remove atom 24024 need remove atom 24028 need remove atom 24030 need remove atom 24036 need remove atom 24068 need remove atom 24072 need remove atom 24074 need remove atom 24080 need remove atom 24112 need remove atom 24116 need remove atom 24118 need remove atom 24124 need remove atom 24156 need remove atom 24160 need remove atom 24162 need remove atom 24168 need remove atom 24200 need remove atom 24204 need remove atom 24206 need remove atom 24212 need remove atom 24244 need remove atom 24248 need remove atom 24250 need remove atom 24256 need remove atom 24288 need remove atom 24292 need remove atom 24294 need remove atom 24300 need remove atom 24332 need remove atom 24336 need remove atom 24338 need remove atom 24344 need remove atom 24376 need remove atom 24380 need remove atom 24382 need remove atom 24388 need remove atom 24420 need remove atom 24424 need remove atom 24426 need remove atom 24432 need remove atom 24464 need remove atom 24468 need remove atom 24470 need remove atom 24476 need remove atom 24508 need remove atom 24512 need remove atom 24514 need remove atom 24520 need remove atom 24552 need remove atom 24556 need remove atom 24558 need remove atom 24564 need remove atom 24596 need remove atom 24600 need remove atom 24602 need remove atom 24608 need remove atom 24640 need remove atom 24644 need remove atom 24646 need remove atom 24652 need remove atom 24684 need remove atom 24688 need remove atom 24690 need remove atom 24696 need remove atom 24728 need remove atom 24732 need remove atom 24734 need remove atom 24740 need remove atom 24772 need remove atom 24776 need remove atom 24778 need remove atom 24784 need remove atom 24816 need remove atom 24820 need remove atom 24822 need remove atom 24828 need remove atom 24860 need remove atom 24864 need remove atom 24866 need remove atom 24872 need remove atom 24904 need remove atom 24908 need remove atom 24910 need remove atom 24916 need remove atom 24948 need remove atom 24952 need remove atom 24954 need remove atom 24960 need remove atom 24992 need remove atom 24996 need remove atom 24998 need remove atom 25004 need remove atom 25036 need remove atom 25040 need remove atom 25042 need remove atom 25048 need remove atom 25080 need remove atom 25084 need remove atom 25086 need remove atom 25092 need remove atom 25124 need remove atom 25128 need remove atom 25130 need remove atom 25136 need remove atom 25168 need remove atom 25172 need remove atom 25174 need remove atom 25180 need remove atom 25212 need remove atom 25216 need remove atom 25218 need remove atom 25224 need remove atom 25256 need remove atom 25260 need remove atom 25262 need remove atom 25268 need remove atom 25300 need remove atom 25304 need remove atom 25306 need remove atom 25312 need remove atom 25344 need remove atom 25348 need remove atom 25350 need remove atom 25356 need remove atom 25388 need remove atom 25392 need remove atom 25394 need remove atom 25400 need remove atom 25432 need remove atom 25436 need remove atom 25438 need remove atom 25444 need remove atom 25476 need remove atom 25480 need remove atom 25482 need remove atom 25488 need remove atom 25520 need remove atom 25524 need remove atom 25526 need remove atom 25532 need remove atom 25564 need remove atom 25568 need remove atom 25570 need remove atom 25576 need remove atom 25608 need remove atom 25612 need remove atom 25614 need remove atom 25620 need remove atom 25652 need remove atom 25656 need remove atom 25658 need remove atom 25664 need remove atom 25696 need remove atom 25700 need remove atom 25702 need remove atom 25708 need remove atom 25740 need remove atom 25744 need remove atom 25746 need remove atom 25752 need remove atom 25784 need remove atom 25788 need remove atom 25790 need remove atom 25796 need remove atom 25828 need remove atom 25832 need remove atom 25834 need remove atom 25840 need remove atom 25872 need remove atom 25876 need remove atom 25878 need remove atom 25884 need remove atom 25916 need remove atom 25920 need remove atom 25922 need remove atom 25928 need remove atom 25960 need remove atom 25964 need remove atom 25966 need remove atom 25972 need remove atom 26004 need remove atom 26008 need remove atom 26010 need remove atom 26016 need remove atom 26048 need remove atom 26052 need remove atom 26054 need remove atom 26060 need remove atom 26092 need remove atom 26096 need remove atom 26098 need remove atom 26104 need remove atom 26136 need remove atom 26140 need remove atom 26142 need remove atom 26148 need remove atom 26180 need remove atom 26184 need remove atom 26186 need remove atom 26192 need remove atom 26224 need remove atom 26228 need remove atom 26230 need remove atom 26236 need remove atom 26268 need remove atom 26272 need remove atom 26274 need remove atom 26280 need remove atom 26312 need remove atom 26316 need remove atom 26318 need remove atom 26324 need remove atom 26356 need remove atom 26360 need remove atom 26362 need remove atom 26368 need remove atom 26400 need remove atom 26412 need remove atom 26444 need remove atom 26456 need remove atom 26488 need remove atom 26500 need remove atom 26532 need remove atom 26544 [I] need removenum=320 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 2.7200239548e-01 8.5293435575e-02 -3.6854575150e-01 dub= -2.8527311756e-01 8.5295345813e-02 3.7535937294e-01 duc= 2.7200316756e-01 -8.6393793339e-02 -3.6854693353e-01 [I] overall tilt ux= -5.5727551304e-01 1.9102376684e-06 7.4390512444e-01 uy= 7.7207491306e-07 -1.7168722891e-01 -1.1820266759e-06 [I] storedr[0]= -1.8629831196e-02 -5.5606595968e-04 -3.8667066789e-02 [I] originally 56320 atoms [I] insert 0 atoms [I] now 56320 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 56320 atoms [I] remove 320 atoms [I] now 56000 atoms [I] NP=56000 n=56000 [I] ASSIGN finalcnfile = dipole_3.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_3.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_3.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 18:14:43 2023 CPU time spent: 4.769851 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue May 30 18:17:33 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1433900296688 [I] ASSIGN makecnspec = -3 [I] ASSIGN makecnspec(1) = -3 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 9 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 45 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 3 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -3 -1 1 -3 1 1 2 0 3]; basis=[ 0.909091 0 0.227273 0 0 0.681818 0.5 0.0454545 0 1 0.863636 0.5 0.0909091 0 2 0.772727 0.5 0.318182 0 3 0.954545 0.5 0.363636 0 4 0.863636 0.5 0.590909 0 5 0.954545 0.5 0.863636 0 6 0.545455 0 0.136364 0 7 0.727273 0 0.181818 0 8 0.636364 0 0.409091 0 9 0.818182 0 0.454545 0 10 0.727273 0 0.681818 0 11 0.909091 0 0.727273 0 12 0.818182 0 0.954545 0 13 0.5 0.5 0 0 14 0.409091 0.5 0.227273 0 15 0.590909 0.5 0.272727 0 16 0.5 0.5 0.5 0 17 0.681818 0.5 0.545455 0 18 0.590909 0.5 0.772727 0 19 0.772727 0.5 0.818182 0 20 0.181818 0 0.0454545 0 21 0.363636 0 0.0909091 0 22 0.272727 0 0.318182 0 23 0.454545 0 0.363636 0 24 0.363636 0 0.590909 0 25 0.545455 0 0.636364 0 26 0.454545 0 0.863636 0 27 0.636364 0 0.909091 0 28 0.0454545 0.5 0.136364 0 29 0.227273 0.5 0.181818 0 30 0.136364 0.5 0.409091 0 31 0.318182 0.5 0.454545 0 32 0.227273 0.5 0.681818 0 33 0.409091 0.5 0.727273 0 34 0.318182 0.5 0.954545 0 35 0 0 0 0 36 0.0909091 0 0.272727 0 37 0 0 0.5 0 38 0.181818 0 0.545455 0 39 0.0909091 0 0.772727 0 40 0.272727 0 0.818182 0 41 0.0454545 0.5 0.636364 0 42 0.136364 0.5 0.909091 0 43 ]; [I] makecn: _NP=71280 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.01010101010101 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.056818181818182 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27878513552049 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.0101010101e-02 -0.0000000000e+00 -5.6818181818e-02 b= 1.3403460122e+00 0.0000000000e+00 -2.3694193859e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.3403460122209 by=0 pxpa=1.326943e+02 pxpb=0.000000e+00 pypb=2.000441e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 33631 need remove atom 33650 need remove atom 33675 need remove atom 33694 need remove atom 33719 need remove atom 33738 need remove atom 33763 need remove atom 33782 need remove atom 33807 need remove atom 33816 need remove atom 33819 need remove atom 33826 need remove atom 33851 need remove atom 33860 need remove atom 33863 need remove atom 33870 need remove atom 33895 need remove atom 33904 need remove atom 33907 need remove atom 33914 need remove atom 33939 need remove atom 33948 need remove atom 33951 need remove atom 33958 need remove atom 33983 need remove atom 33992 need remove atom 33995 need remove atom 34002 need remove atom 34027 need remove atom 34036 need remove atom 34039 need remove atom 34046 need remove atom 34071 need remove atom 34080 need remove atom 34083 need remove atom 34090 need remove atom 34115 need remove atom 34124 need remove atom 34127 need remove atom 34134 need remove atom 34159 need remove atom 34168 need remove atom 34171 need remove atom 34178 need remove atom 34203 need remove atom 34212 need remove atom 34215 need remove atom 34222 need remove atom 34247 need remove atom 34256 need remove atom 34259 need remove atom 34266 need remove atom 34291 need remove atom 34300 need remove atom 34303 need remove atom 34310 need remove atom 34335 need remove atom 34344 need remove atom 34347 need remove atom 34354 need remove atom 34379 need remove atom 34388 need remove atom 34391 need remove atom 34398 need remove atom 34423 need remove atom 34432 need remove atom 34435 need remove atom 34442 need remove atom 34467 need remove atom 34476 need remove atom 34479 need remove atom 34486 need remove atom 34511 need remove atom 34520 need remove atom 34523 need remove atom 34530 need remove atom 34555 need remove atom 34564 need remove atom 34567 need remove atom 34574 need remove atom 34599 need remove atom 34608 need remove atom 34611 need remove atom 34618 need remove atom 34643 need remove atom 34652 need remove atom 34655 need remove atom 34662 need remove atom 34687 need remove atom 34696 need remove atom 34699 need remove atom 34706 need remove atom 34731 need remove atom 34740 need remove atom 34743 need remove atom 34750 need remove atom 34775 need remove atom 34784 need remove atom 34787 need remove atom 34794 need remove atom 34819 need remove atom 34828 need remove atom 34831 need remove atom 34838 need remove atom 34863 need remove atom 34872 need remove atom 34875 need remove atom 34882 need remove atom 34907 need remove atom 34916 need remove atom 34919 need remove atom 34926 need remove atom 34951 need remove atom 34960 need remove atom 34963 need remove atom 34970 need remove atom 34995 need remove atom 35004 need remove atom 35007 need remove atom 35014 need remove atom 35039 need remove atom 35048 need remove atom 35051 need remove atom 35058 need remove atom 35083 need remove atom 35092 need remove atom 35095 need remove atom 35102 need remove atom 35127 need remove atom 35136 need remove atom 35139 need remove atom 35146 need remove atom 35171 need remove atom 35180 need remove atom 35183 need remove atom 35190 need remove atom 35215 need remove atom 35224 need remove atom 35227 need remove atom 35234 need remove atom 35259 need remove atom 35268 need remove atom 35271 need remove atom 35278 need remove atom 35303 need remove atom 35312 need remove atom 35315 need remove atom 35322 need remove atom 35347 need remove atom 35356 need remove atom 35359 need remove atom 35366 need remove atom 35391 need remove atom 35400 need remove atom 35403 need remove atom 35410 need remove atom 35435 need remove atom 35444 need remove atom 35447 need remove atom 35454 need remove atom 35479 need remove atom 35488 need remove atom 35491 need remove atom 35498 need remove atom 35523 need remove atom 35532 need remove atom 35535 need remove atom 35542 need remove atom 35567 need remove atom 35576 need remove atom 35579 need remove atom 35586 need remove atom 35611 need remove atom 35620 need remove atom 35623 need remove atom 35630 need remove atom 35655 need remove atom 35664 need remove atom 35667 need remove atom 35674 need remove atom 35699 need remove atom 35708 need remove atom 35711 need remove atom 35718 need remove atom 35743 need remove atom 35752 need remove atom 35755 need remove atom 35762 need remove atom 35787 need remove atom 35796 need remove atom 35799 need remove atom 35806 need remove atom 35831 need remove atom 35840 need remove atom 35843 need remove atom 35850 need remove atom 35875 need remove atom 35884 need remove atom 35887 need remove atom 35894 need remove atom 35919 need remove atom 35928 need remove atom 35931 need remove atom 35938 need remove atom 35963 need remove atom 35972 need remove atom 35975 need remove atom 35982 need remove atom 36007 need remove atom 36016 need remove atom 36019 need remove atom 36026 need remove atom 36051 need remove atom 36060 need remove atom 36063 need remove atom 36070 need remove atom 36095 need remove atom 36104 need remove atom 36107 need remove atom 36114 need remove atom 36139 need remove atom 36148 need remove atom 36151 need remove atom 36158 need remove atom 36183 need remove atom 36192 need remove atom 36195 need remove atom 36202 need remove atom 36227 need remove atom 36236 need remove atom 36239 need remove atom 36246 need remove atom 36271 need remove atom 36280 need remove atom 36283 need remove atom 36290 need remove atom 36315 need remove atom 36324 need remove atom 36327 need remove atom 36334 need remove atom 36359 need remove atom 36368 need remove atom 36371 need remove atom 36378 need remove atom 36403 need remove atom 36412 need remove atom 36415 need remove atom 36422 need remove atom 36447 need remove atom 36456 need remove atom 36459 need remove atom 36466 need remove atom 36491 need remove atom 36500 need remove atom 36503 need remove atom 36510 need remove atom 36535 need remove atom 36544 need remove atom 36547 need remove atom 36554 need remove atom 36579 need remove atom 36588 need remove atom 36591 need remove atom 36598 need remove atom 36623 need remove atom 36632 need remove atom 36635 need remove atom 36642 need remove atom 36667 need remove atom 36676 need remove atom 36679 need remove atom 36686 need remove atom 36711 need remove atom 36720 need remove atom 36723 need remove atom 36730 need remove atom 36755 need remove atom 36764 need remove atom 36767 need remove atom 36774 need remove atom 36799 need remove atom 36808 need remove atom 36811 need remove atom 36818 need remove atom 36843 need remove atom 36852 need remove atom 36855 need remove atom 36862 need remove atom 36887 need remove atom 36896 need remove atom 36899 need remove atom 36906 need remove atom 36931 need remove atom 36940 need remove atom 36943 need remove atom 36950 need remove atom 36975 need remove atom 36984 need remove atom 36987 need remove atom 36994 need remove atom 37019 need remove atom 37028 need remove atom 37031 need remove atom 37038 need remove atom 37063 need remove atom 37072 need remove atom 37075 need remove atom 37082 need remove atom 37107 need remove atom 37116 need remove atom 37119 need remove atom 37126 need remove atom 37151 need remove atom 37160 need remove atom 37163 need remove atom 37170 need remove atom 37195 need remove atom 37204 need remove atom 37207 need remove atom 37214 need remove atom 37239 need remove atom 37248 need remove atom 37251 need remove atom 37258 need remove atom 37283 need remove atom 37292 need remove atom 37295 need remove atom 37302 need remove atom 37327 need remove atom 37336 need remove atom 37339 need remove atom 37346 need remove atom 37371 need remove atom 37380 need remove atom 37383 need remove atom 37390 need remove atom 37415 need remove atom 37424 need remove atom 37427 need remove atom 37434 need remove atom 37459 need remove atom 37468 need remove atom 37471 need remove atom 37478 need remove atom 37503 need remove atom 37512 need remove atom 37515 need remove atom 37522 need remove atom 37547 need remove atom 37556 need remove atom 37559 need remove atom 37566 need remove atom 37591 need remove atom 37600 need remove atom 37603 need remove atom 37610 need remove atom 37635 need remove atom 37644 need remove atom 37647 need remove atom 37654 [I] need removenum=360 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 2.7200239548e-01 8.5293435575e-02 -3.6854575150e-01 dub= -2.8527311756e-01 8.5295345813e-02 3.7535937294e-01 duc= 2.7200316756e-01 -8.6393793339e-02 -3.6854693353e-01 [I] overall tilt ux= -5.5727551304e-01 1.9102376688e-06 7.4390512444e-01 uy= 7.7207491284e-07 -1.7168722891e-01 -1.1820266748e-06 [I] storedr[0]= -1.7322374807e-02 -5.5610199308e-04 -3.4614297224e-02 [I] originally 71280 atoms [I] insert 0 atoms [I] now 71280 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 71280 atoms [I] remove 360 atoms [I] now 70920 atoms [I] NP=70920 n=70920 [I] ASSIGN finalcnfile = dipole_4.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_4.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_4.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 18:17:40 2023 CPU time spent: 6.041448 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue May 30 18:20:45 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1433900296688 [I] ASSIGN makecnspec = -3 [I] ASSIGN makecnspec(1) = -3 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 10 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 50 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 3 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -3 -1 1 -3 1 1 2 0 3]; basis=[ 0.909091 0 0.227273 0 0 0.681818 0.5 0.0454545 0 1 0.863636 0.5 0.0909091 0 2 0.772727 0.5 0.318182 0 3 0.954545 0.5 0.363636 0 4 0.863636 0.5 0.590909 0 5 0.954545 0.5 0.863636 0 6 0.545455 0 0.136364 0 7 0.727273 0 0.181818 0 8 0.636364 0 0.409091 0 9 0.818182 0 0.454545 0 10 0.727273 0 0.681818 0 11 0.909091 0 0.727273 0 12 0.818182 0 0.954545 0 13 0.5 0.5 0 0 14 0.409091 0.5 0.227273 0 15 0.590909 0.5 0.272727 0 16 0.5 0.5 0.5 0 17 0.681818 0.5 0.545455 0 18 0.590909 0.5 0.772727 0 19 0.772727 0.5 0.818182 0 20 0.181818 0 0.0454545 0 21 0.363636 0 0.0909091 0 22 0.272727 0 0.318182 0 23 0.454545 0 0.363636 0 24 0.363636 0 0.590909 0 25 0.545455 0 0.636364 0 26 0.454545 0 0.863636 0 27 0.636364 0 0.909091 0 28 0.0454545 0.5 0.136364 0 29 0.227273 0.5 0.181818 0 30 0.136364 0.5 0.409091 0 31 0.318182 0.5 0.454545 0 32 0.227273 0.5 0.681818 0 33 0.409091 0.5 0.727273 0 34 0.318182 0.5 0.954545 0 35 0 0 0 0 36 0.0909091 0 0.272727 0 37 0 0 0.5 0 38 0.181818 0 0.545455 0 39 0.0909091 0 0.772727 0 40 0.272727 0 0.818182 0 41 0.0454545 0.5 0.636364 0 42 0.136364 0.5 0.909091 0 43 ]; [I] makecn: _NP=110000 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.0090909090909091 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.045454545454545 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27878513552049 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 9.0909090909e-03 -0.0000000000e+00 -4.5454545455e-02 b= 1.3403460122e+00 0.0000000000e+00 -2.3694193859e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.3403460122209 by=0 pxpa=1.474381e+02 pxpb=0.000000e+00 pypb=2.222712e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 46860 need remove atom 46862 need remove atom 46865 need remove atom 46872 need remove atom 46904 need remove atom 46906 need remove atom 46909 need remove atom 46916 need remove atom 46948 need remove atom 46950 need remove atom 46953 need remove atom 46960 need remove atom 46992 need remove atom 46994 need remove atom 46997 need remove atom 47004 need remove atom 47036 need remove atom 47038 need remove atom 47041 need remove atom 47048 need remove atom 47080 need remove atom 47082 need remove atom 47085 need remove atom 47092 need remove atom 47124 need remove atom 47126 need remove atom 47129 need remove atom 47136 need remove atom 47168 need remove atom 47170 need remove atom 47173 need remove atom 47180 need remove atom 47212 need remove atom 47214 need remove atom 47217 need remove atom 47224 need remove atom 47256 need remove atom 47258 need remove atom 47261 need remove atom 47268 need remove atom 47300 need remove atom 47302 need remove atom 47305 need remove atom 47312 need remove atom 47344 need remove atom 47346 need remove atom 47349 need remove atom 47356 need remove atom 47388 need remove atom 47390 need remove atom 47393 need remove atom 47400 need remove atom 47432 need remove atom 47434 need remove atom 47437 need remove atom 47444 need remove atom 47476 need remove atom 47478 need remove atom 47481 need remove atom 47488 need remove atom 47520 need remove atom 47522 need remove atom 47525 need remove atom 47532 need remove atom 47564 need remove atom 47566 need remove atom 47569 need remove atom 47576 need remove atom 47608 need remove atom 47610 need remove atom 47613 need remove atom 47620 need remove atom 47652 need remove atom 47654 need remove atom 47657 need remove atom 47664 need remove atom 47696 need remove atom 47698 need remove atom 47701 need remove atom 47708 need remove atom 47740 need remove atom 47742 need remove atom 47745 need remove atom 47752 need remove atom 47784 need remove atom 47786 need remove atom 47789 need remove atom 47796 need remove atom 47828 need remove atom 47830 need remove atom 47833 need remove atom 47840 need remove atom 47872 need remove atom 47874 need remove atom 47877 need remove atom 47884 need remove atom 47916 need remove atom 47918 need remove atom 47921 need remove atom 47928 need remove atom 47960 need remove atom 47962 need remove atom 47965 need remove atom 47972 need remove atom 48004 need remove atom 48006 need remove atom 48009 need remove atom 48016 need remove atom 48048 need remove atom 48050 need remove atom 48053 need remove atom 48060 need remove atom 48092 need remove atom 48094 need remove atom 48097 need remove atom 48104 need remove atom 48136 need remove atom 48138 need remove atom 48141 need remove atom 48148 need remove atom 48180 need remove atom 48182 need remove atom 48185 need remove atom 48192 need remove atom 48224 need remove atom 48226 need remove atom 48229 need remove atom 48236 need remove atom 48268 need remove atom 48270 need remove atom 48273 need remove atom 48280 need remove atom 48312 need remove atom 48314 need remove atom 48317 need remove atom 48324 need remove atom 48356 need remove atom 48358 need remove atom 48361 need remove atom 48368 need remove atom 48400 need remove atom 48402 need remove atom 48405 need remove atom 48412 need remove atom 48444 need remove atom 48446 need remove atom 48449 need remove atom 48456 need remove atom 48488 need remove atom 48490 need remove atom 48493 need remove atom 48500 need remove atom 48532 need remove atom 48534 need remove atom 48537 need remove atom 48544 need remove atom 48576 need remove atom 48578 need remove atom 48581 need remove atom 48588 need remove atom 48620 need remove atom 48622 need remove atom 48625 need remove atom 48632 need remove atom 48664 need remove atom 48666 need remove atom 48669 need remove atom 48676 need remove atom 48708 need remove atom 48710 need remove atom 48713 need remove atom 48720 need remove atom 48752 need remove atom 48754 need remove atom 48757 need remove atom 48764 need remove atom 48796 need remove atom 48798 need remove atom 48801 need remove atom 48808 need remove atom 48840 need remove atom 48842 need remove atom 48845 need remove atom 48852 need remove atom 48884 need remove atom 48886 need remove atom 48889 need remove atom 48896 need remove atom 48928 need remove atom 48930 need remove atom 48933 need remove atom 48940 need remove atom 48972 need remove atom 48974 need remove atom 48977 need remove atom 48984 need remove atom 49016 need remove atom 49018 need remove atom 49021 need remove atom 49028 need remove atom 49060 need remove atom 49062 need remove atom 49065 need remove atom 49072 need remove atom 49104 need remove atom 49106 need remove atom 49109 need remove atom 49116 need remove atom 49148 need remove atom 49150 need remove atom 49153 need remove atom 49160 need remove atom 49192 need remove atom 49194 need remove atom 49197 need remove atom 49204 need remove atom 49236 need remove atom 49238 need remove atom 49241 need remove atom 49248 need remove atom 49280 need remove atom 49282 need remove atom 49285 need remove atom 49292 need remove atom 49324 need remove atom 49326 need remove atom 49329 need remove atom 49336 need remove atom 49368 need remove atom 49370 need remove atom 49373 need remove atom 49380 need remove atom 49412 need remove atom 49414 need remove atom 49417 need remove atom 49424 need remove atom 49456 need remove atom 49458 need remove atom 49461 need remove atom 49468 need remove atom 49500 need remove atom 49502 need remove atom 49505 need remove atom 49512 need remove atom 49544 need remove atom 49546 need remove atom 49549 need remove atom 49556 need remove atom 49588 need remove atom 49590 need remove atom 49593 need remove atom 49600 need remove atom 49632 need remove atom 49634 need remove atom 49637 need remove atom 49644 need remove atom 49676 need remove atom 49678 need remove atom 49681 need remove atom 49688 need remove atom 49720 need remove atom 49722 need remove atom 49725 need remove atom 49732 need remove atom 49764 need remove atom 49766 need remove atom 49769 need remove atom 49776 need remove atom 49808 need remove atom 49810 need remove atom 49813 need remove atom 49820 need remove atom 49852 need remove atom 49854 need remove atom 49857 need remove atom 49864 need remove atom 49896 need remove atom 49898 need remove atom 49901 need remove atom 49908 need remove atom 49940 need remove atom 49942 need remove atom 49945 need remove atom 49952 need remove atom 49984 need remove atom 49986 need remove atom 49989 need remove atom 49996 need remove atom 50028 need remove atom 50030 need remove atom 50033 need remove atom 50040 need remove atom 50072 need remove atom 50074 need remove atom 50077 need remove atom 50084 need remove atom 50116 need remove atom 50118 need remove atom 50121 need remove atom 50128 need remove atom 50160 need remove atom 50162 need remove atom 50165 need remove atom 50172 need remove atom 50204 need remove atom 50206 need remove atom 50209 need remove atom 50216 need remove atom 50248 need remove atom 50250 need remove atom 50253 need remove atom 50260 need remove atom 50292 need remove atom 50294 need remove atom 50297 need remove atom 50304 need remove atom 50336 need remove atom 50338 need remove atom 50341 need remove atom 50348 need remove atom 50380 need remove atom 50382 need remove atom 50385 need remove atom 50392 need remove atom 50424 need remove atom 50426 need remove atom 50429 need remove atom 50436 need remove atom 50468 need remove atom 50470 need remove atom 50473 need remove atom 50480 need remove atom 50512 need remove atom 50514 need remove atom 50517 need remove atom 50524 need remove atom 50556 need remove atom 50558 need remove atom 50561 need remove atom 50568 need remove atom 50600 need remove atom 50602 need remove atom 50605 need remove atom 50612 need remove atom 50644 need remove atom 50646 need remove atom 50649 need remove atom 50656 need remove atom 50688 need remove atom 50690 need remove atom 50693 need remove atom 50700 need remove atom 50732 need remove atom 50734 need remove atom 50737 need remove atom 50744 need remove atom 50776 need remove atom 50778 need remove atom 50781 need remove atom 50788 need remove atom 50820 need remove atom 50822 need remove atom 50825 need remove atom 50832 need remove atom 50864 need remove atom 50866 need remove atom 50869 need remove atom 50876 need remove atom 50908 need remove atom 50910 need remove atom 50913 need remove atom 50920 need remove atom 50952 need remove atom 50954 need remove atom 50957 need remove atom 50964 need remove atom 50996 need remove atom 50998 need remove atom 51001 need remove atom 51008 need remove atom 51040 need remove atom 51042 need remove atom 51045 need remove atom 51052 need remove atom 51084 need remove atom 51086 need remove atom 51089 need remove atom 51096 need remove atom 51128 need remove atom 51130 need remove atom 51133 need remove atom 51140 need remove atom 51172 need remove atom 51174 need remove atom 51177 need remove atom 51184 need remove atom 51216 need remove atom 51218 need remove atom 51221 need remove atom 51228 need remove atom 51260 need remove atom 51262 need remove atom 51265 need remove atom 51272 need remove atom 51304 need remove atom 51306 need remove atom 51309 need remove atom 51316 need remove atom 51348 need remove atom 51350 need remove atom 51353 need remove atom 51360 need remove atom 51392 need remove atom 51394 need remove atom 51397 need remove atom 51404 need remove atom 51436 need remove atom 51438 need remove atom 51441 need remove atom 51448 need remove atom 51480 need remove atom 51482 need remove atom 51485 need remove atom 51492 need remove atom 51524 need remove atom 51526 need remove atom 51529 need remove atom 51536 need remove atom 51568 need remove atom 51570 need remove atom 51573 need remove atom 51580 need remove atom 51612 need remove atom 51614 need remove atom 51617 need remove atom 51624 need remove atom 51656 need remove atom 51658 need remove atom 51661 need remove atom 51668 need remove atom 51700 need remove atom 51702 need remove atom 51705 need remove atom 51712 need remove atom 51744 need remove atom 51746 need remove atom 51749 need remove atom 51756 need remove atom 51788 need remove atom 51790 need remove atom 51793 need remove atom 51800 need remove atom 51832 need remove atom 51834 need remove atom 51837 need remove atom 51844 need remove atom 51876 need remove atom 51878 need remove atom 51881 need remove atom 51888 need remove atom 51920 need remove atom 51922 need remove atom 51925 need remove atom 51932 need remove atom 51964 need remove atom 51966 need remove atom 51969 need remove atom 51976 need remove atom 52008 need remove atom 52010 need remove atom 52013 need remove atom 52020 need remove atom 52052 need remove atom 52054 need remove atom 52057 need remove atom 52064 need remove atom 52096 need remove atom 52098 need remove atom 52101 need remove atom 52108 need remove atom 52140 need remove atom 52142 need remove atom 52145 need remove atom 52152 need remove atom 52184 need remove atom 52186 need remove atom 52189 need remove atom 52196 need remove atom 52228 need remove atom 52230 need remove atom 52233 need remove atom 52240 need remove atom 52272 need remove atom 52274 need remove atom 52277 need remove atom 52284 need remove atom 52316 need remove atom 52318 need remove atom 52321 need remove atom 52328 [I] need removenum=500 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 2.7200239548e-01 8.5293435575e-02 -3.6854575150e-01 dub= -2.8527311756e-01 8.5295345813e-02 3.7535937294e-01 duc= 2.7200316756e-01 -8.6393793339e-02 -3.6854693353e-01 [I] overall tilt ux= -5.5727551304e-01 1.9102376695e-06 7.4390512444e-01 uy= 7.7207491295e-07 -1.7168722891e-01 -1.1820266758e-06 [I] storedr[0]= -1.6267065193e-02 -5.5590094627e-04 -3.1218887733e-02 [I] originally 110000 atoms [I] insert 0 atoms [I] now 110000 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 110000 atoms [I] remove 500 atoms [I] now 109500 atoms [I] NP=109500 n=109500 [I] ASSIGN finalcnfile = dipole_4.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_4.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_4.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 18:20:56 2023 CPU time spent: 9.355471 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue May 30 18:26:21 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1433900296688 [I] ASSIGN makecnspec = -3 [I] ASSIGN makecnspec(1) = -3 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 11 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 55 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 3 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -3 -1 1 -3 1 1 2 0 3]; basis=[ 0.909091 0 0.227273 0 0 0.681818 0.5 0.0454545 0 1 0.863636 0.5 0.0909091 0 2 0.772727 0.5 0.318182 0 3 0.954545 0.5 0.363636 0 4 0.863636 0.5 0.590909 0 5 0.954545 0.5 0.863636 0 6 0.545455 0 0.136364 0 7 0.727273 0 0.181818 0 8 0.636364 0 0.409091 0 9 0.818182 0 0.454545 0 10 0.727273 0 0.681818 0 11 0.909091 0 0.727273 0 12 0.818182 0 0.954545 0 13 0.5 0.5 0 0 14 0.409091 0.5 0.227273 0 15 0.590909 0.5 0.272727 0 16 0.5 0.5 0.5 0 17 0.681818 0.5 0.545455 0 18 0.590909 0.5 0.772727 0 19 0.772727 0.5 0.818182 0 20 0.181818 0 0.0454545 0 21 0.363636 0 0.0909091 0 22 0.272727 0 0.318182 0 23 0.454545 0 0.363636 0 24 0.363636 0 0.590909 0 25 0.545455 0 0.636364 0 26 0.454545 0 0.863636 0 27 0.636364 0 0.909091 0 28 0.0454545 0.5 0.136364 0 29 0.227273 0.5 0.181818 0 30 0.136364 0.5 0.409091 0 31 0.318182 0.5 0.454545 0 32 0.227273 0.5 0.681818 0 33 0.409091 0.5 0.727273 0 34 0.318182 0.5 0.954545 0 35 0 0 0 0 36 0.0909091 0 0.272727 0 37 0 0 0.5 0 38 0.181818 0 0.545455 0 39 0.0909091 0 0.772727 0 40 0.272727 0 0.818182 0 41 0.0454545 0.5 0.636364 0 42 0.136364 0.5 0.909091 0 43 ]; [I] makecn: _NP=133100 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.0082644628099174 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.045454545454545 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27878513552049 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 8.2644628099e-03 -0.0000000000e+00 -4.5454545455e-02 b= 1.3403460122e+00 0.0000000000e+00 -2.3694193859e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.3403460122209 by=0 pxpa=1.621819e+02 pxpb=0.000000e+00 pypb=2.444984e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 63595 need remove atom 63602 need remove atom 63605 need remove atom 63614 need remove atom 63639 need remove atom 63646 need remove atom 63649 need remove atom 63658 need remove atom 63683 need remove atom 63690 need remove atom 63693 need remove atom 63702 need remove atom 63727 need remove atom 63734 need remove atom 63737 need remove atom 63746 need remove atom 63771 need remove atom 63778 need remove atom 63781 need remove atom 63790 need remove atom 63815 need remove atom 63822 need remove atom 63825 need remove atom 63834 need remove atom 63859 need remove atom 63866 need remove atom 63869 need remove atom 63878 need remove atom 63903 need remove atom 63910 need remove atom 63913 need remove atom 63922 need remove atom 63947 need remove atom 63954 need remove atom 63957 need remove atom 63966 need remove atom 63991 need remove atom 63998 need remove atom 64001 need remove atom 64010 need remove atom 64035 need remove atom 64042 need remove atom 64045 need remove atom 64054 need remove atom 64079 need remove atom 64086 need remove atom 64089 need remove atom 64098 need remove atom 64123 need remove atom 64130 need remove atom 64133 need remove atom 64142 need remove atom 64167 need remove atom 64174 need remove atom 64177 need remove atom 64186 need remove atom 64211 need remove atom 64218 need remove atom 64221 need remove atom 64230 need remove atom 64255 need remove atom 64262 need remove atom 64265 need remove atom 64274 need remove atom 64299 need remove atom 64306 need remove atom 64309 need remove atom 64318 need remove atom 64343 need remove atom 64350 need remove atom 64353 need remove atom 64362 need remove atom 64387 need remove atom 64394 need remove atom 64397 need remove atom 64406 need remove atom 64431 need remove atom 64438 need remove atom 64441 need remove atom 64450 need remove atom 64475 need remove atom 64482 need remove atom 64485 need remove atom 64494 need remove atom 64519 need remove atom 64526 need remove atom 64529 need remove atom 64538 need remove atom 64563 need remove atom 64570 need remove atom 64573 need remove atom 64582 need remove atom 64607 need remove atom 64614 need remove atom 64617 need remove atom 64626 need remove atom 64651 need remove atom 64658 need remove atom 64661 need remove atom 64670 need remove atom 64695 need remove atom 64702 need remove atom 64705 need remove atom 64714 need remove atom 64739 need remove atom 64746 need remove atom 64749 need remove atom 64758 need remove atom 64783 need remove atom 64790 need remove atom 64793 need remove atom 64802 need remove atom 64827 need remove atom 64834 need remove atom 64837 need remove atom 64846 need remove atom 64871 need remove atom 64878 need remove atom 64881 need remove atom 64890 need remove atom 64915 need remove atom 64922 need remove atom 64925 need remove atom 64934 need remove atom 64959 need remove atom 64966 need remove atom 64969 need remove atom 64978 need remove atom 65003 need remove atom 65010 need remove atom 65013 need remove atom 65022 need remove atom 65047 need remove atom 65054 need remove atom 65057 need remove atom 65066 need remove atom 65091 need remove atom 65098 need remove atom 65101 need remove atom 65110 need remove atom 65135 need remove atom 65142 need remove atom 65145 need remove atom 65154 need remove atom 65179 need remove atom 65186 need remove atom 65189 need remove atom 65198 need remove atom 65223 need remove atom 65230 need remove atom 65233 need remove atom 65242 need remove atom 65267 need remove atom 65274 need remove atom 65277 need remove atom 65286 need remove atom 65311 need remove atom 65318 need remove atom 65321 need remove atom 65330 need remove atom 65355 need remove atom 65362 need remove atom 65365 need remove atom 65374 need remove atom 65399 need remove atom 65406 need remove atom 65409 need remove atom 65418 need remove atom 65443 need remove atom 65450 need remove atom 65453 need remove atom 65462 need remove atom 65487 need remove atom 65494 need remove atom 65497 need remove atom 65506 need remove atom 65531 need remove atom 65538 need remove atom 65541 need remove atom 65550 need remove atom 65575 need remove atom 65582 need remove atom 65585 need remove atom 65594 need remove atom 65619 need remove atom 65626 need remove atom 65629 need remove atom 65638 need remove atom 65663 need remove atom 65670 need remove atom 65673 need remove atom 65682 need remove atom 65707 need remove atom 65714 need remove atom 65717 need remove atom 65726 need remove atom 65751 need remove atom 65758 need remove atom 65761 need remove atom 65770 need remove atom 65795 need remove atom 65802 need remove atom 65805 need remove atom 65814 need remove atom 65839 need remove atom 65846 need remove atom 65849 need remove atom 65858 need remove atom 65883 need remove atom 65890 need remove atom 65893 need remove atom 65902 need remove atom 65927 need remove atom 65934 need remove atom 65937 need remove atom 65946 need remove atom 65971 need remove atom 65978 need remove atom 65981 need remove atom 65990 need remove atom 66015 need remove atom 66022 need remove atom 66025 need remove atom 66034 need remove atom 66059 need remove atom 66066 need remove atom 66069 need remove atom 66078 need remove atom 66103 need remove atom 66110 need remove atom 66113 need remove atom 66122 need remove atom 66147 need remove atom 66154 need remove atom 66157 need remove atom 66166 need remove atom 66191 need remove atom 66198 need remove atom 66201 need remove atom 66210 need remove atom 66235 need remove atom 66242 need remove atom 66245 need remove atom 66254 need remove atom 66279 need remove atom 66286 need remove atom 66289 need remove atom 66298 need remove atom 66323 need remove atom 66330 need remove atom 66333 need remove atom 66342 need remove atom 66367 need remove atom 66374 need remove atom 66377 need remove atom 66386 need remove atom 66411 need remove atom 66418 need remove atom 66421 need remove atom 66430 need remove atom 66455 need remove atom 66462 need remove atom 66465 need remove atom 66474 need remove atom 66499 need remove atom 66506 need remove atom 66509 need remove atom 66518 need remove atom 66543 need remove atom 66550 need remove atom 66553 need remove atom 66562 need remove atom 66587 need remove atom 66594 need remove atom 66597 need remove atom 66606 need remove atom 66631 need remove atom 66638 need remove atom 66641 need remove atom 66650 need remove atom 66675 need remove atom 66682 need remove atom 66685 need remove atom 66694 need remove atom 66719 need remove atom 66726 need remove atom 66729 need remove atom 66738 need remove atom 66763 need remove atom 66770 need remove atom 66773 need remove atom 66782 need remove atom 66807 need remove atom 66814 need remove atom 66817 need remove atom 66826 need remove atom 66851 need remove atom 66858 need remove atom 66861 need remove atom 66870 need remove atom 66895 need remove atom 66902 need remove atom 66905 need remove atom 66914 need remove atom 66939 need remove atom 66946 need remove atom 66949 need remove atom 66958 need remove atom 66983 need remove atom 66990 need remove atom 66993 need remove atom 67002 need remove atom 67027 need remove atom 67034 need remove atom 67037 need remove atom 67046 need remove atom 67071 need remove atom 67078 need remove atom 67081 need remove atom 67090 need remove atom 67115 need remove atom 67122 need remove atom 67125 need remove atom 67134 need remove atom 67159 need remove atom 67166 need remove atom 67169 need remove atom 67178 need remove atom 67203 need remove atom 67210 need remove atom 67213 need remove atom 67222 need remove atom 67247 need remove atom 67254 need remove atom 67257 need remove atom 67266 need remove atom 67291 need remove atom 67298 need remove atom 67301 need remove atom 67310 need remove atom 67335 need remove atom 67342 need remove atom 67345 need remove atom 67354 need remove atom 67379 need remove atom 67386 need remove atom 67389 need remove atom 67398 need remove atom 67423 need remove atom 67430 need remove atom 67433 need remove atom 67442 need remove atom 67467 need remove atom 67474 need remove atom 67477 need remove atom 67486 need remove atom 67511 need remove atom 67518 need remove atom 67521 need remove atom 67530 need remove atom 67555 need remove atom 67562 need remove atom 67565 need remove atom 67574 need remove atom 67599 need remove atom 67606 need remove atom 67609 need remove atom 67618 need remove atom 67643 need remove atom 67650 need remove atom 67653 need remove atom 67662 need remove atom 67687 need remove atom 67694 need remove atom 67697 need remove atom 67706 need remove atom 67731 need remove atom 67738 need remove atom 67741 need remove atom 67750 need remove atom 67775 need remove atom 67782 need remove atom 67785 need remove atom 67794 need remove atom 67819 need remove atom 67826 need remove atom 67829 need remove atom 67838 need remove atom 67863 need remove atom 67870 need remove atom 67873 need remove atom 67882 need remove atom 67907 need remove atom 67914 need remove atom 67917 need remove atom 67926 need remove atom 67951 need remove atom 67958 need remove atom 67961 need remove atom 67970 need remove atom 67995 need remove atom 68002 need remove atom 68005 need remove atom 68014 need remove atom 68039 need remove atom 68046 need remove atom 68049 need remove atom 68058 need remove atom 68083 need remove atom 68090 need remove atom 68093 need remove atom 68102 need remove atom 68127 need remove atom 68134 need remove atom 68137 need remove atom 68146 need remove atom 68171 need remove atom 68178 need remove atom 68181 need remove atom 68190 need remove atom 68215 need remove atom 68222 need remove atom 68225 need remove atom 68234 need remove atom 68259 need remove atom 68266 need remove atom 68269 need remove atom 68278 need remove atom 68303 need remove atom 68310 need remove atom 68313 need remove atom 68322 need remove atom 68347 need remove atom 68354 need remove atom 68357 need remove atom 68366 need remove atom 68391 need remove atom 68398 need remove atom 68401 need remove atom 68410 need remove atom 68435 need remove atom 68442 need remove atom 68445 need remove atom 68454 need remove atom 68479 need remove atom 68486 need remove atom 68489 need remove atom 68498 need remove atom 68523 need remove atom 68530 need remove atom 68533 need remove atom 68542 need remove atom 68567 need remove atom 68574 need remove atom 68577 need remove atom 68586 need remove atom 68611 need remove atom 68618 need remove atom 68621 need remove atom 68630 need remove atom 68655 need remove atom 68662 need remove atom 68665 need remove atom 68674 need remove atom 68699 need remove atom 68706 need remove atom 68709 need remove atom 68718 need remove atom 68743 need remove atom 68750 need remove atom 68753 need remove atom 68762 need remove atom 68787 need remove atom 68794 need remove atom 68797 need remove atom 68806 need remove atom 68831 need remove atom 68838 need remove atom 68841 need remove atom 68850 need remove atom 68875 need remove atom 68882 need remove atom 68885 need remove atom 68894 need remove atom 68919 need remove atom 68926 need remove atom 68929 need remove atom 68938 need remove atom 68963 need remove atom 68970 need remove atom 68973 need remove atom 68982 need remove atom 69007 need remove atom 69014 need remove atom 69017 need remove atom 69026 need remove atom 69051 need remove atom 69058 need remove atom 69061 need remove atom 69070 need remove atom 69095 need remove atom 69102 need remove atom 69105 need remove atom 69114 need remove atom 69139 need remove atom 69146 need remove atom 69149 need remove atom 69158 need remove atom 69183 need remove atom 69190 need remove atom 69193 need remove atom 69202 need remove atom 69227 need remove atom 69234 need remove atom 69237 need remove atom 69246 need remove atom 69271 need remove atom 69278 need remove atom 69281 need remove atom 69290 need remove atom 69315 need remove atom 69322 need remove atom 69325 need remove atom 69334 need remove atom 69359 need remove atom 69366 need remove atom 69369 need remove atom 69378 need remove atom 69403 need remove atom 69410 need remove atom 69413 need remove atom 69422 need remove atom 69447 need remove atom 69454 need remove atom 69457 need remove atom 69466 need remove atom 69491 need remove atom 69498 need remove atom 69501 need remove atom 69510 need remove atom 69542 need remove atom 69545 need remove atom 69586 need remove atom 69589 need remove atom 69630 need remove atom 69633 need remove atom 69674 need remove atom 69677 need remove atom 69718 need remove atom 69721 [I] need removenum=550 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 2.7200239548e-01 8.5293435575e-02 -3.6854575150e-01 dub= -2.8527311756e-01 8.5295345813e-02 3.7535937294e-01 duc= 2.7200316756e-01 -8.6393793339e-02 -3.6854693353e-01 [I] overall tilt ux= -5.5727551304e-01 1.9102376688e-06 7.4390512444e-01 uy= 7.7207491306e-07 -1.7168722891e-01 -1.1820266768e-06 [I] storedr[0]= -1.5399025189e-02 -5.5560823543e-04 -2.8348743433e-02 [I] originally 133100 atoms [I] insert 0 atoms [I] now 133100 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 133100 atoms [I] remove 550 atoms [I] now 132550 atoms [I] NP=132550 n=132550 [I] ASSIGN finalcnfile = dipole_5.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_5.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_5.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 18:26:34 2023 CPU time spent: 11.318998 s {"realtime":1451.54,"usertime":3438.01,"systime":37.78,"memmax":139784,"memavg":0}